#!/usr/bin/python
"""Search for motifs begins from here."""

import sys
from alignment import Alignment, Bucket
#from sequence import Sequence

a = Alignment(sys.argv[1])
d = 5
n = 600
l = 15

l_mers = []

seq = a.sequences[0]

for i in xrange(n-l+1):
    l_mer = seq[i:i+l]
    l_mers.append(l_mer)

# this will contain list of all possible n buckets.
buckets = []

for l_mer in l_mers:
    buckets.append(Bucket([l_mer]))
    


for i in xrange(1, len(a.sequences)):
    seq = a.sequences[i]
    l_mers = []
    
    for i in xrange(n-l+1):
        l_mer = seq[i:i+l]
        l_mers.append(l_mer)
    
    